Diagnosis of cancer, classification of tumors, and cancer-patient prognosis all depend on detection of properties inherent to cancer, or malignant cells, that are absent in normal, nonmalignant cells. Since cancer is largely a genetic disease, resulting from and associated with changes in the DNA of cells, one important method of diagnosis is through detection of related changes within the DNA of cancer cells. Such changes can be of two types. The first type of change is a genetic change that occurs when the sequence of nucleotide bases within the DNA is changed. Base changes, deletions and insertions in the DNA are examples of such genetic changes. The second type of change in the DNA is an epigenetic change. Epigenetic changes do not result in nucleotide sequence changes, but rather, result in modification of nucleotide bases. The most common type of epigenetic change is DNA methylation.
In mammalian cells, DNA methylation consists exclusively of addition of a methyl group to the 5-carbon position of cytosine nucleotide bases. In the process, cytosine is changed to 5-methylcytosine. Cellular enzymes carry out the methylation events. Only cytosines located 5′ to guanosines in CpG dinucleotides are methylated by the enzymes in mammalian cells. Such CpG dinucleotides are not distributed randomly throughout the genome. Instead, there are regions of mammalian genomes which contain many CpG dinucleotides, while other areas of the genome contain few CpG dinucleotides. Such CpG-rich areas of the genome are called “CpG islands.” Most often, CpG islands are located in the transcriptional promoter regions of genes.
Not all CpG islands are methylated However, the methylation status of CpG islands (i.e., whether the CpG dinucleotides within a particular CpG island are methylated or not) is relatively constant in cells. Nevertheless, the pattern of CpG island methylation can change and, when it does, often a new, relatively stable methylation pattern is established. Such changes in methylation of CpG islands can be either increases or decreases in methylation.
Methylation of CpG islands in the promoter region of a few specific genes has been observed in some types of human cancer. However, at present it is still uncertain whether the methylation status of multiple CpG islands in the genomic DNA of subjects suspected of having cancer can be used as a diagnostic tool for determining whether or not tissue obtained from such subjects contain malignant cells.